Update README

README.md

@@ -1,4 +1,4 @@
-# Euromix model to SBML
+# EuroMix model to SBML
 
 This repository contains a re-implementation of the [EuroMix PBK model](https://doi.org/10.1016/j.fct.2020.111440) in [Antimony](https://tellurium.readthedocs.io/en/latest/antimony.html) and demonstrates how this Antimony model implementation is automatically converted to an annotated Systems Biology Markup Language ([SBML](https://sbml.org/)) file using the [SBML PBK workflow](https://github.com/jwkruisselbrink/sbml-pbk-workflow). The purpose of this repository is to test/demonstrate how to create and publish interoperable PBK models using the EuroMix PBK model as example.
 
@@ -12,11 +12,15 @@ The model was reimplemented in [Antimony](https://tellurium.readthedocs.io/en/la
 
 Notebook [validate_antimony_model.ipynb](notebooks/validate_antimony_model.ipynb) shows the results of the validation comparison with the results obtained by the R/MCSim/desolve implementation. Note that the [libRoadRunner](https://www.libroadrunner.org/) engine that is used for the python simulations returns concentrations, also if a species is declared to be `substanceOnly`. Therefore it is necessary to convert the output to amounts by multiplying the concentration with volume of the compartment the species is placed in in order to obtain amounts.
 
-## SBML conversion and annotation
+## Model annotation
 
-The [SBML PBK workflow](https://github.com/jwkruisselbrink/sbml-pbk-workflow) follows several steps. It first converts the Antimony model implementation to SBML. Then, it annotates this SBML file using the annotations specified in the file [euromix.annotations.csv](model/euromix.annotations.csv). After this, it runs (unit) validation scripts on the generated SBML file. Finally, it publishes the generated SBML file (and log files) as build artifacts and pushes the generated/updated sbml file ([euromix.sbml](model/euromix.sbml)) to the repository.
+Annotations of the model and its element are specified in the file [euromix.annotations.csv](model/euromix.annotations.csv). This annotations file links the different model elements (e.g., compartments and parameters) to ontological terms and, where relevant, specifies the units of measure. For the annotations of modelling terms, the [BPBK ontology](http://obofoundry.org/ontology/pbpko) is used. For the annotation of the units of measure,  the [UCUM](https://ucum.org/) notation is adopted.
 
-Notebook [get_model_info.ipynb](notebooks/get_model_info.ipynb) shows how information can be retrieved from the annotated model (e.g., units, differential equations, diagrams, semantic annotations). Notebook [run_sbml_model.ipynb](notebooks/run_sbml_model.ipynb) demonstrates how to run the SBML model.
+## SBML conversion and SBML model annotation
+
+The [SBML PBK workflow](https://github.com/jwkruisselbrink/sbml-pbk-workflow) follows several steps. It first converts the Antimony model implementation to SBML. Then, it annotates this SBML file using the annotations specified in the [euromix.annotations.csv](model/euromix.annotations.csv) file. After this, it runs (unit) validation scripts on the generated SBML file. Finally, it publishes the generated SBML file (and log files) as build artifacts and pushes the generated/updated sbml file ([euromix.sbml](model/euromix.sbml)) to the repository.
+
+Notebook [get_model_info.ipynb](notebooks/get_model_info.ipynb) shows how information can be retrieved from the annotated SBML model file (e.g., units, differential equations, diagrams, semantic annotations). Notebook [run_sbml_model.ipynb](notebooks/run_sbml_model.ipynb) demonstrates how to run the SBML model.
 
 ## Running the Jupyter notebooks